I understand that i have to perform the same filtering/approach on all data-sets in order to compare them properly. In order to do this it is essential to have uniform data-sets. This is most likely not the case for two of the data-sets so i will have to find a way to make them uniform.

In the tutorial HTSFilter is used , but it can not be performed on data-sets with no replicates. My problem is that i really want to use all the data-sets.